A codon is a three nucleotide sequence that codes for an amino acid.

Codon Usage Bias

While the codons that code for a particular amino acid result in highly similar behavior during translation, one codon can result in greater gene expression or more efficient translation than another. Over time, and as the result of mutations (single nucleotide polymorphisms), alignment for more efficient codons can occur, resulting in codon optimization.

Researchers have noted that the genomes of viruses adapt to align with their host's codon usage bias.1) 2)

Codon Optimization

Codon optimization occurs when the codon present out of several synonymous codons

October 13, 2009 | Iris Bahir et al | Mol Syst Biol. (journal) | Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences | doi: 10.1038/msb.2009.71
November 28, 2016 | Hongju Wang et al | PLoS One (journal) | Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts | doi: 10.1371/journal.pone.0166260